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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4tp1



4TP1 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin. this file contains the 50s subunit of the first 70s ribosome with dalfopristin bound.
List of all 66 Mg2+ binding sites in the PDB structure 4tp1 in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 1 of 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tp1 B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94
4tp1 A3115 Ob U:A1602(O4) A3713, A3714, A3715, A3716 A:A1342 G:A1601
4tp1 A3073 Ob C:A2499(O2) A3533, A3534, A3535, A3536, A3537 G:A2032 C:A2055, U:A2500, G:A2454, G:A2032
4tp1 A3090 Ob G:A1125(O6) A3608, A3609, A3610, A3611, A3612 G:A1124
4tp1 A3102 Ob U:A2419(O4) A3669, A3670, 3101, 3102, 3103 A:A2418
4tp1 A3079 Oph A:A299(OP2) A3557, A3558, A3559, A3560, U201 U:A339, A:A299, G:A338
4tp1 A3008 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4tp1 A3028 Oph A:A800(OP1) A3326, A3327, A3328, A3329, A3330 G:A799 A:A191, C:A192, A:A800
4tp1 A3054 Oph·Pout A:A1678(OP2) A3440, A3441, A3442, A3443, A3444 A:A1679 A:A1678, A:A1679
4tp1 A3099 Oph·Pout C:A1658(OP1) A3655, A3656, A3657, D302, D303 G:A1659 A:A743
4tp1 A3004 Oph·Pout U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A121 G:A122, G:A123
4tp1 A3051 Oph·Pout A:A1664(OP2) A3425, A3426, A3427, A3428, A3429 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4tp1 A3034 Oph·Pout A:A945(OP1) A3353, A3354, A3355, A3356, A3357 G:A831 G:A831, U:A832
4tp1 A3135 Oph·Pout A:A943(OP2) A3793, A3794, A3795, L206, L207 U:A832
4tp1 B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B101 A:B73 A:B101, G:B102
4tp1 A3015 Oph·Pout A:A574(OP2) A3265, A3266, A3267, A3268, A3269 U:A573 U:A576, G:A577
4tp1 A3077 Oph·2Pout G:A2714(OP2) A3550, A3551, A3552, N201 A:A2711, C:A2710
4tp1 A3060 Oph·2Pout A:A1970(OP2) A3470, A3471, A3472, A3473, A3474 A:A1900, G:A1835 U:A1834 G:A1835, C:A1836
4tp1 A3036 Oph·2Pout U:A999(OP2) A3361, A3362, A3363, A3364 C:A1153, C:A998
4tp1 A3029 Oph·2Pout A:A802(OP1) A3331, A3332, A3333, A3334, A3335 A:A675, G:A674 U:A803, A:A804

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"		 Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen 		cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform 		Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>